That's not what an EEZ is for (despite what the Chinese may think). UNCLOS provides for enforcement of domestic laws in EEZ only with regard to the exploration, exploitation, and conservation of living resources. The legality of the blockade is not really in dispute, but you don't have to make up rights of seizure in EEZ's or sovereign rights (i.e. border control) to a territory Israel asserts it no longer occupies to defend that claim.
What's at stake here is not the legality of the blockade but how far Israel is willing to go to enforce it. It was completely rational to resist - the convoy wanted to see and document how far Israel would escalate. The legality of the blockade doesn't resolve the subjective question of the level of force appropriate to enforce it. Despite the rhetoric about Israelis not caring about public opinion (external or internal), they clearly did not want to kill people to stop a convoy of food, medicine, and construction materials - hence why they went in with non-lethal means. Yet they let themselves get goaded into a very bad position, compounded by their own tactical mishandling of the situation.